\(^1\) Plateau technique de biologie
moléculaire et bioinformatique, INCI - LNCA, Strasbourg
\(^2\) Équipe Modulation
épigénétique des processus neurodégénératifs, LNCA, Strasbourg
- Log in to Galaxy

- History
- Create a New
History

- Rename the History
to “DNA-seq data analysis”
- Change the name of the new history to “DNA-seq data analysis” by
clicking the pencil icon next to the history name.
- Click on “Unnamed history” at the top of the history panel, enter
“DNA-seq data analysis,” and click Save.

- Importing Files from
Your Computer to Galaxy
- Download the file sample.bed.gz from this link
and upload it to Galaxy.
- Genome: Mouse (mm9)
- Format: bed
- Ensure you are in the “DNA-seq data analysis” history (switch to it
if needed).
- Upload Steps:
- Download the file sample.bed.gz.
- Upload it into Galaxy under the “DNA-seq data analysis” history:
- Click on Upload Data.
- Drag and drop the file into the upload window.
- Set:
- Genome: Mouse (mm9)
- Format: bed

- Remove a Dataset
- Remove the sample.bed.gz dataset from your history
by clicking the delete button.

- Verify that your history is empty:
- Click Show deleted at the top of the history
panel.
- Permanently delete the file by clicking Purge All Deleted
Content.
- Return to the active view by clicking Show
active.

- Create a Workflow Out
of an Existing History
- Extract a workflow from the “DNA-seq data analysis” history:
- Go to the history menu and select Extract
Workflow.

- Rename the workflow to “DNA-seq data analysis.”

- Edit a Workflow with
the Workflow Editor
- Open the DNA-seq data analysis workflow in the
editor:
- Go to Workflows (top menu/side bar) and select
Edit.

- Add the following tools to the workflow:
- Samtools flagstat (compute mapping statistics after
BWA mem).
- Filter SAM or BAM (remove low-quality reads with
MAPQ < 20).
- Samtools flagstat (compute mapping statistics after
filtering).
- Rename CRN-107_11-R1.fastq.gz box to Read 1 (fastq).
- Rename CRN-107_11-R2.fastq.gz box to Read 2 (fastq).
- Rename CaptureDesign_chr4.bed box to Capture Design (bed).
- Save the workflow.

- Run a Workflow
- Copy the following files to a new history:
- CRN-107_11-R1.fastq.gz
- CRN-107_11-R2.fastq.gz
- CaptureDesign_chr4.bed
- Run the DNA-seq data analysis workflow:
- Select the appropriate input files and parameters.

- How many reads are discarded due to low mapping quality?
- In case of
emergency
The final history can be imported from here